Phylogenetic models and model selection for noncoding DNA

Abstract

Awareness of the complex structure and evolutionary dynamics of noncoding DNA has improved both noncoding sequence alignment and the use of microstructural changes as characters in phylogenetic analysis. The next step is to consider improvements in the use and selection of phylogenetic models for noncoding sequence data. Models of character evolution are central to phylogeny estimation, but the use of an inadequate model can mislead topology selection and branch length estimations. This is particularly likely when sequence divergence is either limited (nearly invariable, as in population-level or species-level studies) or extreme (nearly saturated, as in deep-level studies that focus on conserved secondary structures). Noncoding data sets are often at these extremes, and they can be particularly awkward for model definition and model selection. This paper introduces the goals of model use in phylogenetics and identifies ten issues that arise from the application of models to noncoding sequence data. It is concluded that most of these issues derive from small data set sizes, very low or very high sequence variability, limitations of current phylogenetic models, and possibly character definition and nonindependence. Recommendations are made that should help to improve alignment, character quality, model selection, and phylogeny estimation based on noncoding sequence data.

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Acknowledgments

Financial support during the development of this article was provided by National Science Foundation award DEB-0515828 to S.A. Kelchner. The author thanks Sean Graham for his careful comments and prompting during the formation of the manuscript, Amanda Fisher and Chang Liu for their fine-tuning of the text, an anonymous reviewer for insightful suggestions that clarified several of the issues discussed, and Thomas Borsch, Dietmar Quandt and the German Science Foundation for their kind invitation to present this topic at the 17th International Symposium on Biodiversity and Evolutionary Biology in Bonn, Germany (September 2006).

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